Evaluation of substrate specificity and catalytic promiscuity of Bacillus albus cellulase: an insight into in silico proteomic study aiming at enhanced production of renewable energy

References

• Antunes, D. A., Moll, M., Devaurs, D., Jackson, K. R., Lizée, G., & Kavraki, L. E. (2017). DINC 2.0: A new protein–peptide docking webserver using an incremental approach. Cancer Research, 77(21), e55–e57. https://doi.org/10.1158/0008-5472.CAN-17-0511
   PubMed Web of Science ®Google Scholar
• Bhatt, P., Deepthi, S., Kumar, C. R. S., & Jha, A. (2017). Facile synthesis, spectral studies, dft calculations and biological activities of novel ni (ii), cu (ii), and pd (ii) complexes of thiadiazole analogs. International Journal of Pharmacy and Pharmaceutical Sciences, 9(4), 185–192. https://doi.org/10.22159/ijpps.2017v9i4.17130
   Google Scholar
• Bianchetti, C. M., Brumm, P., Smith, R. W., Dyer, K., Hura, G. L., Rutkoski, T. J., & Phillips, G. N. (2013). Structure, dynamics, and specificity of endoglucanase D from Clostridium cellulovorans. Journal of Molecular Biology, 425(22), 4267–4285. https://doi.org/10.1016/j.jmb.2013.05.030
   PubMed Web of Science ®Google Scholar
• Bornscheuer, U. T., Huisman, G. W., Kazlauskas, R. J., Lutz, S., Moore, J. C., & Robins, K. (2012). Engineering the third wave of biocatalysis. Nature, 485(7397), 185–194. https://doi.org/10.1038/nature11117
   PubMed Web of Science ®Google Scholar
• Burton, R. A., Gidley, M. J., & Fincher, G. B. (2010). Heterogeneity in the chemistry, structure and function of plant cell walls. Nature Chemical Biology, 6(10), 724–732. https://doi.org/10.1038/nchembio.439
   PubMed Web of Science ®Google Scholar
• Chen, Z., Friedland, G. D., Pereira, J. H., Reveco, S. A., Chan, R., Park, J. I., Thelen, M. P., Adams, P. D., Arkin, A. P., Keasling, J. D., Blanch, H. W., Simmons, B. A., Sale, K. L., Chivian, D., & Chhabra, S. R. (2012). Tracing determinants of dual substrate specificity in glycoside hydrolase family 5. The Journal of Biological Chemistry, 287(30), 25335–25343. https://doi.org/10.1074/jbc.M112.362640
   PubMed Web of Science ®Google Scholar
• Corpet, F. (1988). Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research, 16(22), 10881–10890. https://doi.org/10.1093/nar/16.22.10881
   PubMed Web of Science ®Google Scholar
• Darden, T., Perera, L., Li, L., & Pedersen, L. (1999). New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure, 7(3), R55–R60. https://doi.org/10.1016/s0969-2126(99)80033-1
   PubMed Web of Science ®Google Scholar
• Davids, T., Schmidt, M., Böttcher, D., & Bornscheuer, U. T. (2013). Strategies for the discovery and engineering of enzymes for biocatalysis. Current Opinion in Chemical Biology, 17(2), 215–220. https://doi.org/10.1016/j.cbpa.2013.02.022
   PubMed Web of Science ®Google Scholar
• de Melo-Minardi, R. C., Bastard, K., & Artiguenave, F. (2010). Identification of subfamily-specific sites based on active sites modeling and clustering. Bioinformatics, 26(24), 3075–3082. https://doi.org/10.1093/bioinformatics/btq595
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). The PyMOL molecular graphics system. San Carlos, CA: DeLano Scientific. http://www.pymol.org.
   Google Scholar
• Dennington, I. R., Keith, T. A., & Millam, J. M. (2009). GaussView 5.0. https://doi.org/10.4236/oalib.1103172
   Google Scholar
• Ejaz, U., Sohail, M., & Ghanemi, A. (2021). Cellulases: From bioactivity to a variety of industrial applications. Biomimetics, 6(3), 44. https://doi.org/10.3390/biomimetics6030044
   PubMed Web of Science ®Google Scholar
• Emsley, P., & Cowtan, K. (2004). Coot: Model-building tools for molecular graphics. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 12 Pt 1), 2126–2132. https://doi.org/10.1107/S0907444904019158
   PubMedGoogle Scholar
• Eslami-Farsani, R., Shareghi, B., Farhadian, S., & Momeni, L. (2021). Experimental and theoretical investigations on the interaction of glucose molecules with myoglobin in the aqueous solution using theoretical and experimental methods. Journal of Biomolecular Structure & Dynamics, 39(17), 6384–6395. https://doi.org/10.1080/07391102.2020.1798283
   PubMed Web of Science ®Google Scholar
• Farajzadeh-Dehkordi, N., Farhadian, S., Zahraei, Z., Gholamian-Dehkordi, N. and Shareghi, B. (2021). Interaction of reactive Red195 with human serum albumin: Determination of the binding mechanism and binding site by spectroscopic and molecular modeling methods. Journal of Molecular Liquids, 52, 1214. https://doi.org/10.1016/j.molliq.2020.114835
   Google Scholar
• Fernandes, J., Gattass, C. R. (2009) Topological polar surface area defines substrate transport by multidrug resistance associated protein 1 (MRP1/ABCC1). Journal of Medicinal Chemistry 52(4), 1214–1218.
   PubMed Web of Science ®Google Scholar
• Fokas, A. S., Cole, D. J., Ahnert, S. E., & Chin, A. W. (2016). Residue geometry networks: A rigidity-based approach to the amino acid network and evolutionary rate analysis. Scientific Reports, 6(1), 33213. https://doi.org/10.1038/srep33213
   PubMedGoogle Scholar
• Foresman, J., & Frish, E. (1996). Exploring chemistry. Gaussian Inc.
   Google Scholar
• Frisch, M. J. E. A. (2009). Gaussian 09 (Vol. 32, pp. 5648–5652). Gaussian, Inc.
   Google Scholar
• Garg, R., Srivastava, R., Brahma, V., Verma, L., Karthikeyan, S., & Sahni, G. (2016). Biochemical and structural characterization of a novel halotolerant cellulase from soil metagenome. Scientific Reports, 6(1), 39634. https://doi.org/10.1038/srep39634
   PubMedGoogle Scholar
• Guérin, D. M. A., Lascombe, M.-B., Costabel, M., Souchon, H., Lamzin, V., Béguin, P., & Alzari, P. M. (2002). Atomic (0.94 Å) resolution structure of an inverting glycosidase in complex with substrate. Journal of Molecular Biology, 316(5), 1061–1069. https://doi.org/10.1006/jmbi.2001.5404
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Himmel, M. E., Ding, S.-Y., Johnson, D. K., Adney, W. S., Nimlos, M. R., Brady, J. W., & Foust, T. D. (2007). Biomass recalcitrance: Engineering plants and enzymes for biofuels production. Science, 315(5813), 804–807. https://doi.org/10.1126/science.1137016
   PubMed Web of Science ®Google Scholar
• Himmel, M. E., & Himmel, M. E. (2008). Biomass recalcitrance: Deconstructing the plant cell wall for bioenergy. Blackwell.
   Google Scholar
• Horn, S. J., Sikorski, P., Cederkvist, J. B., Vaaje-Kolstad, G., Sørlie, M., Synstad, B., Vriend, G., Vårum, K. M., & Eijsink, V. G. (2006). Costs and benefits of processivity in enzymatic degradation of recalcitrant polysaccharides. Proceedings of the National Academy of Sciences of the United States of America, 103(48), 18089–18094. https://doi.org/10.1073/pnas.0608909103
   PubMed Web of Science ®Google Scholar
• Katouno, F., Taguchi, M., Sakurai, K., Uchiyama, T., Nikaidou, N., Nonaka, T., Sugiyama, J., & Watanabe, T. (2004). Importance of exposed aromatic residues in chitinase B from Serratia marcescens 2170 for crystalline chitin hydrolysis. Journal of Biochemistry, 136(2), 163–168. https://doi.org/10.1093/jb/mvh105
   PubMed Web of Science ®Google Scholar
• Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870–1874. https://doi.org/10.1093/molbev/msw054
   PubMed Web of Science ®Google Scholar
• Kurniawan, D. W., Storm, G., Prakash, J., & Bansal, R. (2020). Role of spleen tyrosine kinase in liver diseases. World Journal of Gastroenterology, 26(10), 1005–1019. https://doi.org/10.3748/wjg.v26.i10.1005
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., Jabłońska, J., Pravda, L., Vařeková, R. S., & Thornton, J. M. (2018). PDBsum: Structural summaries of PDB entries. Protein Science: A Publication of the Protein Society, 27(1), 129–134. https://doi.org/10.1002/pro.3289
   PubMed Web of Science ®Google Scholar
• Le Guilloux, V., Schmidtke, P., & Tuffery, P. (2009). Fpocket: An open source platform for ligand pocket detection. BMC Bioinformatics, 10(1), 168. https://doi.org/10.1186/1471-2105-10-168
   PubMed Web of Science ®Google Scholar
• Lee, D., Redfern, O., & Orengo, C. (2007). Predicting protein function from sequence and structure. Nature Reviews. Molecular Cell Biology, 8(12), 995–1005. https://doi.org/10.1017/s0033583503003901
   PubMed Web of Science ®Google Scholar
• Lin, L., Yan, R., Liu, Y., & Jiang, W. (. (2010). In-depth investigation of enzymatic hydrolysis of biomass wastes based on three major components: Cellulose, hemicellulose and lignin. Bioresource Technology, 101(21), 8217–8223. https://doi.org/10.1016/j.biortech.2010.05.084
   PubMed Web of Science ®Google Scholar
• Lindahl, E., Azuara, C., Koehl, P., & Delarue, M. (2006). NOMAD-Ref: Visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Research, 34(Web Server issue), W52–W56. https://doi.org/10.1093/nar/gkl082
   PubMed Web of Science ®Google Scholar
• Lucas, M. C., Bhagirath, N., Chiao, E., Goldstein, D. M., Hermann, J. C., Hsu, P.-Y., Kirchner, S., Kennedy-Smith, J. J., Kuglstatter, A., Lukacs, C., Menke, J., Niu, L., Padilla, F., Peng, Y., Polonchuk, L., Railkar, A., Slade, M., Soth, M., Xu, D., … Liao, C. (2014). Using ovality to predict nonmutagenic, orally efficacious pyridazine amides as cell specific spleen tyrosine kinase inhibitors. Journal of Medicinal Chemistry, 57(6), 2683–2691. https://doi.org/10.1021/jm401982j
   PubMed Web of Science ®Google Scholar
• Mitra, D. (2018). Quantum mechanical descriptors of nilotinib’s impurities. Quantum, 6(1), 1–8.
   Google Scholar
• Mitra, D., & Bose, A. (2021). Remarkable effect of natural compounds that have therapeutic effect to stop COVID-19. Recent Advances in Pharmaceutical Sciences, 115–126.
   Google Scholar
• Mitra, D., Dey, A., Biswas, I., & Das Mohapatra, P. K. (2021). Bioactive compounds as a potential inhibitor of colorectal cancer; an in silico study of Gallic acid and Pyrogallol. Iranian Journal of Colorectal Research, 9(1), 32–39. https://doi.org/10.30476/acrr.2021.89642.1080
   Google Scholar
• Mitra, D., Paul, M., Thatoi, H., & Mohapatra, P. K. (2021). Study of potentiality of dexamethasone and its derivatives against Covid-19. Journal of Biomolecular Structure & Dynamics, 40(20), 10239–10249. https://doi.org/10.1080/07391102.2021.1942210
   PubMed Web of Science ®Google Scholar
• Miyamoto, S., & Kollman, P. A. (1992). SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13(8), 952–962. https://doi.org/10.1002/jcc.540130805
   Web of Science ®Google Scholar
• Mohammadi, M., Shareghi, B., Farhadian, S., & Saboury, A. A. (2021). The effect of sorbitol on the structure and activity of carboxypeptidase A: Insights from a spectroscopic and computational approach. Journal of Molecular Liquids, 330, 115710. https://doi.org/10.1016/j.molliq.2021.115710
   Web of Science ®Google Scholar
• Nakamura, A., Watanabe, H., Ishida, T., Uchihashi, T., Wada, M., Ando, T., Igarashi, K., & Samejima, M. (2014). Trade-off between processivity and hydrolytic velocity of cellobiohydrolases at the surface of crystalline cellulose. Journal of the American Chemical Society, 136(12), 4584–4592. https://doi.org/10.1021/ja4119994
   PubMed Web of Science ®Google Scholar
• Páll, S., Abraham, M. J., Kutzner, C., Hess, B., & Lindahl, E. (2015). Tackling exascale software challenges in molecular dynamics simulations with GROMACS. In International conference on exascale applications and software (pp. 3–27). Springer. https://doi.org/10.1007/978-3-319-15976-8_1
   Google Scholar
• Patel, A. K., Singhania, R. R., Sim, S. J., & Pandey, A. (2019). Thermostable cellulases: Current status and perspectives. Bioresource Technology, 279, 385–392. https://doi.org/10.1016/j.biortech.2019.01.049
   PubMed Web of Science ®Google Scholar
• Paul, M., Das Mohapatra, P. K., & Thatoi, H. (2023). Purified cellulase‐mediated simultaneous sugar utilization by Bacillus albus isolated from Similipal, Odisha, India. Journal of Basic Microbiology, 63(7), 759–780. https://doi.org/10.1002/jobm.202300006
   PubMed Web of Science ®Google Scholar
• Paul, M., Mohapatra, S., Mohapatra, P. K. D., & Thatoi, H. (2021). Microbial cellulases–An update towards its surface chemistry, genetic engineering and recovery for its biotechnological potential. Bioresource Technology, 340, 125710. https://doi.org/10.1016/j.biortech.2021.125710
   PubMed Web of Science ®Google Scholar
• Paul, M., Panda, G., Mohapatra, P. K. D., & Thatoi, H. (2020). Study of structural and molecular interaction for the catalytic activity of cellulases: An insight in cellulose hydrolysis for higher bioethanol yield. Journal of Molecular Structure, 1204p., 127547. https://doi.org/10.1016/j.molstruc.2019.127547
   Web of Science ®Google Scholar
• Paul, M., Panda, M. K., & Thatoi, H. (2018). Developing Hispolon-based novel anticancer therapeutics against human (NF-κβ) using in silico approach of modelling, docking and protein dynamics. Journal of Biomolecular Structure & Dynamics, 37(15), 3947–3967. https://doi.org/10.1080/07391102.2018.1532321
   PubMed Web of Science ®Google Scholar
• Pedretti, A., Mazzolari, A., & Vistoli, G. (2008). VEGA ZZ: A versatile toolkit for drug design and protein modelling. In Congreso de FisicoquímicaTeórica y Computacional, https://doi.org/10.1016/S1093-3263(02)00123-7
   Google Scholar
• Pérez, J., Muñoz-Dorado, J., de la Rubia, T., & Martínez, J. (2002). Biodegradation and biological treatments of cellulose, hemicellulose and lignin: An overview. International Microbiology, 5(2), 53–63. https://doi.org/10.1007/s10123-002-0062-3
   PubMedGoogle Scholar
• Piovesan, D., Minervini, G., & Tosatto, S. C. E. (2016). The RING 2.0 web server for high quality residue interaction networks. Nucleic Acids Research, 44(W1), W367–W374. http://protein.bio.unipd.it/ring/. https://doi.org/10.1093/nar/gkw315
   PubMed Web of Science ®Google Scholar
• Prates, É. T., Stankovic, I., Silveira, R. L., Liberato, M. V., Henrique-Silva, F., Pereira, N., Polikarpov, I., & Skaf, M. S. (2013). X-ray structure and molecular dynamics simulations of endoglucanase 3 from Trichoderma harzianum: Structural organization and substrate recognition by endoglucanases that lack cellulose binding module. PloS One, 8(3), e59069. https://doi.org/10.1371/journal.pone.0059069
   PubMed Web of Science ®Google Scholar
• Raeessi-Babaheydari, E., Farhadian, S., & Shareghi, B. (2021). Evaluation of interaction between citrus flavonoid, naringenin, and pepsin using spectroscopic analysis and docking simulation. Journal of Molecular Liquids, 339, 116763. https://doi.org/10.1016/j.molliq.2021.116763
   Web of Science ®Google Scholar
• Rausell, A., Juan, D., Pazos, F., & Valencia, A. (2010). Protein interactions and ligand binding: From protein subfamilies to functional specificity. Proceedings of the National Academy of Sciences of the United States of America, 107(5), 1995–2000. https://doi.org/10.1073/pnas.0908044107
   PubMed Web of Science ®Google Scholar
• Sadeghi-Kaji, S., Shareghi, B., Saboury, A. A., & Farhadian, S. (2020). Investigating the interaction of porcine pancreatic elastase and propanol: A spectroscopy and molecular simulation study. International Journal of Biological Macromolecules, 146, 687–691. https://doi.org/10.1016/j.ijbiomac.2019.12.119
   PubMed Web of Science ®Google Scholar
• Scapin, S. M. N., Souza, F. H. M., Zanphorlin, L. M., de Almeida, T. S., Sade, Y. B., Cardoso, A. M., Pinheiro, G. L., & Murakami, M. T. (2017). Structure and function of a novel GH8 endoglucanase from the bacterial cellulose synthase complex of Raoultella ornithinolytica. PloS One, 12(4), e0176550. https://doi.org/10.1371/journal.pone.0176550
   PubMed Web of Science ®Google Scholar
• Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005). PatchDock and SymmDock: Servers for rigid and symmetric docking. Nucleic Acids Research, 33(Web Server issue), W363–W367. https://doi.org/10.1093/nar/gki481
   PubMed Web of Science ®Google Scholar
• Selvam, K., Senbagam, D., Selvankumar, T., Sudhakar, C., Kamala-Kannan, S., Senthilkumar, B., & Govarthanan, M. (2017). Cellulase enzyme: Homology modeling, binding site identification and molecular docking. J Mol Struct,.1150, 61–67. https://doi.org/10.1016/j.molstruc.2017.08.067
   Web of Science ®Google Scholar
• Sujatha, M. S., & Balaji, P. V. (2004). Identification of common structural features of binding sites in galactose-specific proteins. Proteins, 55(1), 44–65. https://doi.org/10.1002/prot.10612
   PubMed Web of Science ®Google Scholar
• Thatoi, H., Mohapatra, S., Paul, M., Behera, S., & Mahuri, M. (2023). Improvement of saccharification of native grass, Pennisetum sp. using cellulase from isolated Aspergillus fumigatus for bioethanol production: An insight into in silico molecular modelling, docking and dynamics studies. Systems Microbiology and Biomanufacturing, 3(3), 394–413. https://doi.org/10.1007/s43393-022-00114-7
   Google Scholar
• Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673–4680. https://doi.org/10.1093/nar/22.22.4673
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina, Improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Uchiyama, T., Uchihashi, T., Nakamura, A., Watanabe, H., Kaneko, S., Samejima, M., & Igarashi, K. (2020). Convergent evolution of processivity in bacterial and fungal cellulases. Proceedings of the National Academy of Sciences of the United States of America, 117(33), 19896–19903. https://doi.org/10.1073/pnas.2011366117
   PubMed Web of Science ®Google Scholar
• van Gunsteren, W. F. (1996). Biomolecular simulation: The GROMOS96 manual and user guide (Vol. 86, pp. 1–1044). Vdf Hochschulverlag AG an der ETH Zürich.
   Google Scholar
• Vaught, A. (1996). Graphing with Gnuplot and Xmgr: Two graphing packages available under linux. Linux Journal, 1996(28es), 7–es.
   Google Scholar
• Wang, K., Cao, R., Wang, M., Lin, Q., Zhan, R., Xu, H., & Wang, S. (2019). A novel thermostable GH10 xylanase with activities on a wide variety of cellulosic substrates from a xylanolytic Bacillus strain exhibiting significant synergy with commercial Celluclast 1.5 L in pretreated corn stover hydrolysis. Biotechnology for Biofuels, 12(1), 48. https://doi.org/10.1186/s13068-019-1389-8
   PubMedGoogle Scholar
• Wang, W., Archbold, T., Lam, J. S., Kimber, M. S., & Fan, M. Z. (2019). A processive endoglucanase with multi-substrate specificity is characterized from porcine gut microbiota. Scientific Reports, 9(1), 13630. https://doi.org/10.1038/s41598-019-50050-1
   PubMedGoogle Scholar
• Wang, Z., Pan, H., Sun, H., Kang, Y., Liu, H., Cao, D., & Hou, T. (2022). fastDRH: A webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation. Briefings in Bioinformatics, 23(5), bbac201. https://doi.org/10.1093/bib/bbac201
   PubMed Web of Science ®Google Scholar
• Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427
   PubMed Web of Science ®Google Scholar
• Weber, W., Hünenberger, P. H., & McCammon, J. A. (2000). Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation. The Journal of Physical Chemistry B, 104(15), 3668–3675. https://doi.org/10.1021/jp9937757
   Web of Science ®Google Scholar
• Wilson, D. B. (2009). Cellulases and biofuels. Current Opinion in Biotechnology, 20(3), 295–299. https://doi.org/10.1016/j.copbio.2009.05.007
   PubMed Web of Science ®Google Scholar
• Wita, A., Białas, W., Wilk, R., Szychowska, K., & Czaczyk, K. (2019). The influence of temperature and nitrogen source on cellulolytic potential of microbiota isolated from natural environment. Polish Journal of Microbiology, 68(1), 105–114. https://doi.org/10.21307/pjm-2019-012
   PubMed Web of Science ®Google Scholar
• Zakariassen, H., Aam, B. B., Horn, S. J., Vårum, K. M., Sørlie, M., & Eijsink, V. G. H. (2009). Aromatic residues in the catalytic center of chitinase A from Serratia marcescens affect processivity, enzyme activity, and biomass converting efficiency. The Journal of Biological Chemistry, 284(16), 10610–10617. https://doi.org/10.1074/jbc.M900092200
   PubMed Web of Science ®Google Scholar
• Zhang, Y. H. P., Himmel, M. E., & Mielenz, J. R. (2006). Outlook for cellulase improvement: Screening and selection strategies. Biotechnology Advances, 24(5), 452–481. https://doi.org/10.1016/j.biotechadv.2006.03.003
   PubMed Web of Science ®Google Scholar